Deep-Time Phylogenetic Clustering of Extinctions in an Evolutionarily Dynamic Clade (Early Jurassic Ammonites)

Hardy, Clotilde; Fara, Emmanuel; Laffont, Rémi; Dommergues, Jean‐Louis; Meister, Christian; Neige, Pascal

doi:10.1371/journal.pone.0037977

Cited by 21 publications

(39 citation statements)

References 40 publications

(84 reference statements)

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“…Similarities in extinction risk among closely related lineages have been documented across a diversity of groups including frogs , birds (Bennett et al 2005), bivalves (Roy et al 2009a), ammonites (Hardy et al 2012), and brachiopods (this study). This correlation between phylogeny and extinction risk can be explained by similarities among closely related lineages in the biological characteristics that affect the vulnerability of lineages to changing ecological and environmental conditions.…”

Section: Discussionsupporting

confidence: 67%

Phylogenetic signal in extinction selectivity in Devonian terebratulide brachiopods

Harnik¹,

Fitzgerald²,

Payne³

et al. 2014

Paleobiology

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Determining which biological traits affect taxonomic durations is critical for explaining macroevolutionary patterns. Two approaches are commonly used to investigate the associations between traits and durations and/or extinction and origination rates: analyses of taxonomic occurrence patterns in the fossil record and comparative phylogenetic analyses, predominantly of extant taxa. By capitalizing upon the empirical record of past extinctions, paleontological data avoid some of the limitations of existing methods for inferring extinction and origination rates from molecular phylogenies. However, most paleontological studies of extinction selectivity have ignored phylogenetic relationships because there is a dearth of phylogenetic hypotheses for diverse non-vertebrate higher taxa in the fossil record. This omission inflates the degrees of freedom in statistical analyses and leaves open the possibility that observed associations are indirect, reflecting shared evolutionary history rather than the direct influence of particular traits on durations. Here we investigate global patterns of extinction selectivity in Devonian terebratulide brachiopods and compare the results of taxonomic vs. phylogenetic approaches. Regression models that assume independence among taxa provide support for a positive association between geographic range size and genus duration but do not indicate an association between body size and genus duration. Brownian motion models of trait evolution identify significant similarities in body size, range size, and duration among closely related terebratulide genera. We use phylogenetic regression to account for shared evolutionary history and find support for a significant positive association between range size and duration among terebratulides that is also phylogenetically structured. The estimated range size–duration relationship is moderately weaker in the phylogenetic analysis due to the down-weighting of closely related genera that were both broadly distributed and long lived; however, this change in slope is not statistically significant. These results provide evidence for the phylogenetic conservatism of organismal and emergent traits, yet also the general phylogenetic independence of the relationship between range size and duration.

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Section: Discussionsupporting

confidence: 67%

Phylogenetic signal in extinction selectivity in Devonian terebratulide brachiopods

Harnik¹,

Fitzgerald²,

Payne³

et al. 2014

Paleobiology

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“…20). This result agrees with the studies of Dommergues et al (2000) and Hardy et al (2013). These two species are representative of the most basal occurence of the Hildoceratidae.…”

Section: Basal Nodessupporting

confidence: 93%

The phylogeny of Hildoceratidae (Cephalopoda, Ammonitida) resolved by an integrated coding scheme of the conch

2016

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Ammonite phylogeny has mainly been established based on a stratigraphic approach, with cladistics underconsidered. The main arguments against the use of cladistics are the supposed large amount of homoplasy and the small number of characters. Resolving the phylogeny of the Hildoceratidae (Early Jurassic) is especially challenging because of its large diversity and disparity. Many forms that have not been determined as closely related in previous studies exhibit very similar shapes. Moreover, some groups are morphologically very different, adding difficulties to building a unique coding scheme at a low taxonomic resolution (i.e. species). Here we propose an integrated coding scheme of the peristome shape and the ornamentation, allowing an increased level of comparison. The shape of the peristome is used as a new reference to locate ornamental features and propose new homology hypotheses. In total, 105 taxa have been analysed for 47 characters. We code continuous characters by their means and ranges AE one standard deviation. We test two weighting schemes: equal weights standardized by unit range and implied weighting with several concavity constants. This work has led to redefinition of the phylogenetic inclusivenesses of all the hildoceratid subfamilies. The new coding scheme based on peristome shapes provides the fewest homoplastic characters. The schemes appear promising to improve phylogenetic analyses in ammonoids as well as molluscs as a whole by creating a general coding framework.

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“…Thus, existing studies do not readily allow direct comparisons of past losses of EH with those predicted for anthropogenic extinctions. Although temporal durations of species in the fossil record are more difficult to estimate reliably than those of higher taxa (23), a number of paleontological studies have used fossil species successfully to test important evolutionary and biogeographic hypotheses (21,(51)(52)(53)(54)(55)(56) as well as various aspects of the extinction process (57)(58)(59). With the increasing availability of large, taxonomically standardized paleontological databases, analyses of age selectivity of extinctions at the species level, such as the one undertaken here, are now feasible, especially on regional scales.…”

Section: Discussionmentioning

confidence: 99%

Fossils, phylogenies, and the challenge of preserving evolutionary history in the face of anthropogenic extinctions

Huang

Goldberg

Roy

2015

Proc. Natl. Acad. Sci. U.S.A.

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Anthropogenic impacts are endangering many long-lived species and lineages, possibly leading to a disproportionate loss of existing evolutionary history (EH) in the future. However, surprisingly little is known about the loss of EH during major extinctions in the geological past, and thus we do not know whether human impacts are pruning the tree of life in a manner that is unique in the history of life. A major impediment to comparing the loss of EH during past and current extinctions is the conceptual difference in how ages are estimated from paleontological data versus molecular phylogenies. In the former case the age of a taxon is its entire stratigraphic range, regardless of how many daughter taxa it may have produced; for the latter it is the time to the most recent common ancestor shared with another extant taxon. To explore this issue, we use simulations to understand how the loss of EH is manifested in the two data types. We also present empirical analyses of the marine bivalve clade Pectinidae (scallops) during a major Plio-Pleistocene extinction in California that involved a preferential loss of younger species. Overall, our results show that the conceptual difference in how ages are estimated from the stratigraphic record versus molecular phylogenies does not preclude comparisons of age selectivities of past and present extinctions. Such comparisons not only provide fundamental insights into the nature of the extinction process but should also help improve evolutionarily informed models of conservation prioritization.extinction | phylogenetic diversity | phylogeny | fossil record | bivalves E xtinction of any species or higher taxon invariably results in some loss of existing evolutionary history (EH), but a major concern about extinctions driven by anthropogenic impacts is that they may remove a disproportionately large amount of such history (1-3). In groups as varied as birds, mammals, and plants, studies have shown that extinctions of species currently on the International Union for the Conservation of Nature Red List of Threatened Species would lead to a much larger loss of EH than expected under randomly distributed extinction of the same number of species (4-6). This disproportionate loss of EH stems from phylogenetic clustering of anthropogenic extinctions (1) with a bias toward the loss of species-poor and geologically old taxa (7-9). Such predictions, along with the realization that not all species currently threatened by human activities can be saved, have motivated the development of various strategies for minimizing the loss of EH (8, 10, 11). These approaches primarily target lineages that are old but species poor in an attempt to protect large amounts of EH and, presumably, also unique traits and functions that may affect future evolutionary potential (10,12).Although the disproportionate loss of EH caused by anthropogenic extinctions is increasingly evident, surprisingly little is known about the loss of EH during extinctions in the geological past. The rich archive of extinctions pres...

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Deep-Time Phylogenetic Clustering of Extinctions in an Evolutionarily Dynamic Clade (Early Jurassic Ammonites)

Cited by 21 publications

References 40 publications

Phylogenetic signal in extinction selectivity in Devonian terebratulide brachiopods

Phylogenetic signal in extinction selectivity in Devonian terebratulide brachiopods

The phylogeny of Hildoceratidae (Cephalopoda, Ammonitida) resolved by an integrated coding scheme of the conch

Fossils, phylogenies, and the challenge of preserving evolutionary history in the face of anthropogenic extinctions

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